Variant rs13178541 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001349335.2(SLC25A48):c.-116-13487A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,094 control chromosomes in the GnomAD database, including 39,527 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.71 ( 39527 hom., cov: 33)

Consequence

SLC25A48
NM_001349335.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.691

Variant links:

Genes affected

SLC25A48 (HGNC:30451): (solute carrier family 25 member 48) Predicted to enable acyl carnitine transmembrane transporter activity. Predicted to be involved in acyl carnitine transport and amino acid transport. Predicted to be located in mitochondrial inner membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC25A48 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A48	NM_001349335.2 linkuse as main transcript	c.-116-13487A>C		intron_variant			NP_001336264.1
SLC25A48	NM_001349345.2 linkuse as main transcript	c.-116-13487A>C		intron_variant			NP_001336274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A48	ENST00000646290.1 linkuse as main transcript	c.-116-13487A>C		intron_variant				ENSP00000493514

Frequencies

GnomAD3 genomes

AF:

0.712

AC:

108136

AN:

151976

Hom.:

39503

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.893

Gnomad AMR

AF:

0.678

Gnomad ASJ

AF:

0.776

Gnomad EAS

AF:

0.704

Gnomad SAS

AF:

0.732

Gnomad FIN

AF:

0.779

Gnomad MID

AF:

0.829

Gnomad NFE

AF:

0.804

Gnomad OTH

AF:

0.748

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.711

AC:

108206

AN:

152094

Hom.:

39527

Cov.:

AF XY:

0.711

AC XY:

52841

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.542

Gnomad4 AMR

AF:

0.678

Gnomad4 ASJ

AF:

0.776

Gnomad4 EAS

AF:

0.704

Gnomad4 SAS

AF:

0.732

Gnomad4 FIN

AF:

0.779

Gnomad4 NFE

AF:

0.804

Gnomad4 OTH

AF:

0.748

Alfa

AF:

0.687

Hom.:

2435

Bravo

AF:

0.692

Asia WGS

AF:

0.729

AC:

2537

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

6.2

DANN

Benign

0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over